Posts by Johan

... System developer at the NGI-Uppsala SNP&SEQ Technology Platform at the Department of Medical Sciences
As a part of the National Genomics Infrastructure (NGI) at the Science for Life Laboratory (SciLifeLab, https://www.scilifelab.se), the SNP&SEQ Technology Platform in Uppsala provides SNP-ge ...

... Come and join the team at the SNP&SEQ technology platform! We are currently looking for two system developers to help us build the tools for running one of Europe's largest sequencing centers. We work with the latest technology in a cross-disciplinary team to solve exciting problems in the genom ...

... Would you like to work in one of the most rapidly growing application areas in the world? As a bioinformatician at the SNP&SEQ technology platform you will work alongside researchers and system developers in a dynamic and creative atmosphere at one of Europe’s largest sequencing centers. You wil ...

... You can set the directory to read from by:
cuff <- readCufflinks(dir="/path/to/your/data")
However, if I'm not mistaken cummeRbund should be used to read cuffdiff results, i.ex. results from differential expression studies, which means that normally you would have all you output data in one pl ...

... I've been working with Queue for about a year and a half now, and have it deployed in production at our core facility. I find that it strikes a good balance between expressiveness and simplicity. It has good cluster support, will of course play really nicely with all the GATK tools and is easy to ex ...

... Does each sample represent a unique condition? If they are really representatives of different groups you should use the: --labels flag and compare the conditions rather than compare all samples vs. all other samples.
Your command line should end up looking something like this:
cuffdiff --labels C ...

... I've been working some with QScripts, in our pipeline project called Piper. The code is available here on github: https://github.com/johandahlberg/piper
If you want to start off with some simple example I'd recommend looking at MergeBamsBySample. However, there are some more advanced examples in th ...

... I did some experimentation of my own, and just as @Fabio Marroni suggests in his comment to my question the correct way to do it is alternative 1:
cuffdiff <other options> --labels conditionA,conditionB <annotations file> sample1.bam,sample2.bam sample3.bam,sample4.bam
...

... I've been trying to figure out how to setup the cuffdiff command line if one wants both labels and replicates, but I think that the manual could have been more specific on this point. Should there be one label per condition of one per input file. To exemplify:
Assume that I have two conditions A a ...